Article
Multidisciplinary Sciences
Xiaowei Huo, Sisi Liu, Yimin Li, Hao Wei, Jing Gao, Yonggang Yan, Gang Zhang, Mengmeng Liu
Summary: In this study, the nucleotide composition and codon bias parameters of Rheum palmatum genes were analyzed, revealing a higher AT content and a preference for A/T ending codons. Mutation pressure was identified as the primary factor influencing codon bias in R. palmatum, with most optimal codons ending in A or U. This study provides important insights for enhancing gene expression and predicting genetic and evolutionary mechanisms in R. palmatum.
Article
Virology
Zhen He, Shiwen Ding, Jiyuan Guo, Lang Qin, Xiaowei Xu
Summary: This study analyzed the phylogeny and codon usage pattern of narcissus viruses using the coat protein. The results showed that codon usage bias in these viruses is mainly influenced by natural selection, indicating the importance of evolutionary-based design for controlling these viruses.
Article
Virology
Simiao Zhao, Huiqi Cui, Zhenru Hu, Li Du, Xuhua Ran, Xiaobo Wen
Summary: This study reveals the significant impact of synonymous codon mutations on the evolution of the SVA virus and highlights their important role in adapting to adverse environments.
Article
Multidisciplinary Sciences
Xukang Shen, Siliang Song, Chuan Li, Jianzhi Zhang
Summary: Synonymous mutations in protein-coding genes are not neutral and often result in reduced fitness and disturbed mRNA expression levels. Non-synonymous mutations have greater fitness variations across environments, which may explain the lower substitution rates compared to synonymous mutations.
Article
Genetics & Heredity
Alexander C. Cope, Premal Shah
Summary: The research reveals the impact of intragenomic variation in non-adaptive nucleotide bias on natural selection of synonymous codon usage. Unsupervised learning methods can identify genes evolving under different non-adaptive nucleotide biases, which is crucial for understanding codon usage biases.
Article
Biotechnology & Applied Microbiology
Jayanta Kumar Das, Swarup Roy
Summary: This study provides a comprehensive quantitative analysis of the protein-coding sequences of seven human coronaviruses, revealing the nucleotide sequence variability and codon usage patterns. Different categories of codons exhibit diverse adaptability, with notable variability in GC content at the third position among the seven coronaviruses. Phylogenetic analysis depicted the evolutionary relationships among these viruses and their positions in the tree.
Article
Genetics & Heredity
Wenjing Xu, Yingchun Li, Yajing Li, Chun Liu, Yanxia Wang, Guangmin Xia, Mengcheng Wang
Summary: Asymmetric somatic hybridization affects synonymous codon usage bias (SCUB) and promotes a bias towards A- and T-ending synonymous codons, with a stronger effect in indel-flanking sequences. This shift is attributed to whole genomic shock, and DNA methylation may play a role in SCUB shift during asymmetric somatic hybridization. Exogenous chromatin fragments introduced through this strategy do not have a local chromosomal effect on SCUB frequencies.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Ravail Singh
Summary: Research has found that genes in Ancylostoma ceylanicum show an AT bias and have a narrow GC3 distribution, leading to a certain codon usage bias. Analysis indicates that both mutation pressure and evolutionary factors influence the codon usage pattern. Additionally, codon context analysis reveals skewed usage of certain homologous codon pairs in this species.
Article
Biochemistry & Molecular Biology
Konrad Pawlak, Pawel Blazej, Dorota Mackiewicz, Pawel Mackiewicz
Summary: Synonymous codon usage is influenced by mutations and selection at both the nucleotide and amino acid levels. The proposed mutation-selection model demonstrates that the selection of amino acids based on physicochemical properties can result in biases in codon usage. Alternative genetic codes tend to exhibit greater codon bias than the standard genetic code, and the mutational pressures on cytosine and guanine content further affect usage bias. The study emphasizes the importance of considering amino acid selection in understanding codon usage patterns.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Geng Tian, Guilian Xiao, Tong Wu, Junzhi Zhou, Wenjing Xu, Yanxia Wang, Guangmin Xia, Mengcheng Wang
Summary: The diploidization of polyploid genomes is accompanied by genomic variation and synonymous codon usage bias (SCUB). SCUB alters during the formation of hexaploid wheat and contributes to epigenetic variation. DNA methylation-mediated conversion weakens following the increase of genome ploidy, coinciding with the stronger bias for certain codons in hexaploid wheat.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Gun Li, Liang Zhang, Ning Du
Summary: This study compared the relative synonymous codon usage of the ORF1ab gene in SARS-CoV-2 and SARS-CoV, finding significant differences in codon usage between the two viruses. The results suggest that the codon usage pattern of SARS-CoV is more similar to human, while SARS-CoV-2 shows larger internal differences, indicating greater diversity within the virus.
Article
Immunology
Quanming Xu, Hong Chen, Wen Sun, Dewen Zhu, Yongyi Zhang, Ji-Long Chen, Ye Chen
Summary: The study found that the codon usage pattern in Streptococcus suis is influenced by natural selection, showing significant differences in evolution and distinct from the synonymous codon usage of susceptible hosts.
MICROBIAL PATHOGENESIS
(2021)
Article
Immunology
Yu Fan, Duan Guo, Shangping Zhao, Qiang Wei, Yi Li, Tao Lin
Summary: This study aimed to explore the potential involvement of human genes with codon usage bias (CUB) similar to human polyomaviruses (HPyVs) genes in the pathogenesis of polyomavirus nephropathy (PVAN). The analysis revealed a significant correlation between HPyV genes and human genes, with a strong protein-protein interaction network. Gene expression analysis identified differentially expressed genes between normal kidney tissues and PVAN patients, which were involved in transcription, protein ubiquitination pathway, apoptosis, cellular response to stress, inflammation, and immune system. These findings may have implications for the diagnosis and treatment of HPyV-associated diseases, particularly PVAN.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Davide Arella, Maddalena Dilucca, Andrea Giansanti
Summary: This study investigated the relationship between codon usage bias, microbial lifestyles, and habitats in 615 microbial organisms. The results showed that species with similar phenotypic traits living in similar environmental conditions exhibit similar codon preferences and tRNA availability. Additionally, organisms able to live in multiple habitats have reduced translational efficiency.
MOLECULAR GENETICS AND GENOMICS
(2021)
Article
Forestry
Jing Chen, Wuqiang Ma, Xinwen Hu, Kaibing Zhou
Summary: The synonymous codon usage (SCU) bias in oil-tea camellia cpDNAs was analyzed, and a conserved bias was observed among the samples. The third position GC content (GC3) showed a preference for A or T, suggesting weak SCU bias. The correlation analysis revealed the relationship between GC content and expected number of codons (ENC). These findings provide insights for studying cpDNA gene expression and genetic engineering.
Article
Evolutionary Biology
Jonathan Romiguier, Jonathan Rolland, Claire Morandin, Laurent Keller
BMC EVOLUTIONARY BIOLOGY
(2018)
Article
Ecology
Florentine Riquet, Cathy Liautard-Haag, Lucy Woodall, Carmen Bouza, Patrick Louisy, Bojan Hamer, Francisco Otero-Ferrer, Philippe Aublanc, Vickie Beduneau, Olivier Briard, Tahani El Ayari, Sandra Hochscheid, Khalid Belkhir, Sophie Arnaud-Haond, Pierre-Alexandre Gagnaire, Nicolas Bierne
Article
Ecology
Tahani El Ayari, Najoua Trigui El Menif, Bojan Hamer, Abigail E. Cahill, Nicolas Bierne
Article
Biodiversity Conservation
Florentine Riquet, Cathy Lieutard-Haag, Giulia Serluca, Lucy Woodall, Julien Claude, Patrick Louisy, Nicolas Bierne
CONSERVATION GENETICS
(2019)
Article
Evolutionary Biology
Iva Popovic, Ambrocio Melvin A. Matias, Nicolas Bierne, Cynthia Riginos
EVOLUTIONARY APPLICATIONS
(2020)
Article
Evolutionary Biology
Alexis Simon, Christine Arbiol, Einar Eg Nielsen, Jerome Couteau, Rossana Sussarellu, Thierry Burgeot, Ismael Bernard, Joop W. P. Coolen, Jean-Baptiste Lamy, Stephane Robert, Maria Skazina, Petr Strelkov, Henrique Queiroga, Ibon Cancio, John J. Welch, Frederique Viard, Nicolas Bierne
EVOLUTIONARY APPLICATIONS
(2020)
Article
Zoology
E. A. Burioli, S. Trancart, A. Simon, I Bernard, M. Charles, E. Oden, N. Bierne, M. Houssin
JOURNAL OF INVERTEBRATE PATHOLOGY
(2019)
Article
Biology
Marisa A. Yonemitsu, Rachael M. Giersch, Maria Polo-Prieto, Maurine Hammel, Alexis Simon, Florencia Cremonte, Fernando T. Aviles, Nicolas Merino-Veliz, Erika A. V. Burioli, Annette F. Muttray, James Sherry, Carol Reinisch, Susan A. Baldwin, Stephen P. Goff, Maryline Houssin, Gloria Arriagada, Nuria Vazquez, Nicolas Bierne, Michael J. Metzger
Article
Biochemistry & Molecular Biology
Jonathan Rolland, Dolph Schluter, Jonathan Romiguier
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Ecology
Alexis Simon, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John J. Welch, Nicolas Bierne
Summary: The Mytilus complex of marine mussel species forms a mosaic of hybrid zones across temperate regions. The study showed local introgression is widespread and heterogeneous, with some loci near fixation for the heterospecific allele close to hybrid zones. Overall, there is high concordance among loci globally, along with some signals of asymmetric introgression.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2021)
Article
Ecology
Iva Popovic, Nicolas Bierne, Federico Gaiti, Milos Tanurdzic, Cynthia Riginos
Summary: This study investigates genetic parallelism in multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in different regions and with hybridization with a native congener. The results reveal repeatability in differentiation and introgression across genetically distinct lineages, highlighting the impact of demographic histories and pre-introduction introgression on contemporary admixture dynamics. The findings suggest that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Alan Le Moan, Charlotte Roby, Christelle Fraisse, Claire Daguin-Thiebaut, Nicolas Bierne, Frederique Viard
Summary: Anthropogenic hybridization can lead to recent introgression breakthroughs between species, as shown by the recent hybridization events observed between introduced and native Ciona populations. This study highlights the potential evolutionary consequences of human-driven translocations on promoting introgression between previously allopatric taxa.
Article
Evolutionary Biology
Fanny Touchard, Alexis Simon, Nicolas Bierne, Frederique Viard
Summary: Portuarization, the repeated evolution of marine species in port ecosystems under human-altered selective pressures, drives various evolutionary processes including establishment of new connectivity hubs, adaptive responses to new chemicals or biotic communities, and hybridization between lineages. However, there are still important knowledge gaps and further research is needed to understand this phenomenon better.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Multidisciplinary Sciences
Terence Legrand, Anne Chenuil, Enrico Ser-Giacomi, Sophie Arnaud-Haond, Nicolas Bierne, Vincent Rossi
Summary: The study used gene flow to predict genetic differentiation among different populations in the Mediterranean basin, finding that the multi-generational coalescent connectivity model outperformed others significantly, which is of great significance for unraveling the eco-evolutionary forces shaping sedentary population structures.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Murielle Alund, Meredith Cenzer, Nicolas Bierne, Janette W. Boughman, Jose Cerca, Mattheau S. Comerford, Alessandro Culicchi, Brian Langerhans, S. Eryn Mcfarlane, Markus H. Most, Henry North, Anna Qvarnstrom, Mark Ravinet, Richard Svanback, Scott A. Taylor
Summary: Anthropogenic impacts on the environment have both positive and negative effects on speciation processes. Human activities can generate spatial isolation and genetic divergence, but they can also cause sudden secondary contact and hybridization. Changes in the environment created by human actions can create new ecological niches and drive diversification, but they can also lead to niche loss and extinctions. It is important to monitor and understand these impacts in order to promote diversification and enhance biodiversity.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
(2023)